1
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Dao K, Jungers CF, Djuranovic S, Mustoe AM. U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606557. [PMID: 39149310 PMCID: PMC11326173 DOI: 10.1101/2024.08.05.606557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Non-coding RNA sequences play essential roles in orchestrating gene expression. However, the sequence codes and mechanisms underpinning post-transcriptional regulation remain incompletely understood. Here, we revisit the finding from a prior massively parallel reporter assay (MPRA) that AU-rich (U-rich) elements in 3' untranslated regions (3' UTRs) can drive upregulation or downregulation of mRNA expression depending on 3' UTR context. We unexpectedly discover that this variable regulation arises from widespread cryptic splicing, predominately from an unannotated splice donor in the coding sequence of GFP to diverse acceptor sites in reporter 3' UTRs. Splicing is activated by U-rich sequences, which function as potent position-dependent regulators of 5' and 3' splice site choice and overall splicing efficiency. Splicing has diverse impacts on reporter expression, causing both increases and decreases in reporter expression via multiple mechanisms. We further provide evidence that cryptic splicing impacts between 10 to 50% of measurements made by other published 3' UTR MPRAs. Overall, our work emphasizes U-rich sequences as principal drivers of splicing and provides strategies to minimize cryptic splicing artifacts in reporter assays.
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Affiliation(s)
- Khoa Dao
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
| | - Courtney F. Jungers
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine in St. Louis, St. Louis MO
| | - Anthony M. Mustoe
- Therapeutic Innovation Center (THINC), Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston TX
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston TX
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2
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Qin Z, Yang J, Zhang K, Gao X, Ran Q, Xu Y, Wang Z, Lou D, Huang C, Zellmer L, Meng G, Chen N, Ma H, Wang Z, Liao DJ. Updating mRNA variants of the human RSK4 gene and their expression in different stressed situations. Heliyon 2024; 10:e27475. [PMID: 38560189 PMCID: PMC10980951 DOI: 10.1016/j.heliyon.2024.e27475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/11/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
We determined RNA spectrum of the human RSK4 (hRSK4) gene (also called RPS6KA6) and identified 29 novel mRNA variants derived from alternative splicing, which, plus the NCBI-documented ones and the five we reported previously, totaled 50 hRSK4 RNAs that, by our bioinformatics analyses, encode 35 hRSK4 protein isoforms of 35-762 amino acids. Many of the mRNAs are bicistronic or tricistronic for hRSK4. The NCBI-normalized NM_014496.5 and the protein it encodes are designated herein as the Wt-1 mRNA and protein, respectively, whereas the NM_001330512.1 and the long protein it encodes are designated as the Wt-2 mRNA and protein, respectively. Many of the mRNA variants responded differently to different situations of stress, including serum starvation, a febrile temperature, treatment with ethanol or ethanol-extracted clove buds (an herbal medicine), whereas the same stressed situation often caused quite different alterations among different mRNA variants in different cell lines. Mosifloxacin, an antibiotics and also a functional inhibitor of hRSK4, could inhibit the expression of certain hRSK4 mRNA variants. The hRSK4 gene likely uses alternative splicing as a handy tool to adapt to different stressed situations, and the mRNA and protein multiplicities may partly explain the incongruous literature on its expression and comports.
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Affiliation(s)
- Zhenwei Qin
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Jianglin Yang
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
| | - Keyin Zhang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Xia Gao
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Qianchuan Ran
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Yuanhong Xu
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Zhi Wang
- Department of Pathology, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Didong Lou
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Chunhua Huang
- Section of Forensic Science and Pathology, School of Basic Medical Sciences, Guizhou University of Traditional Chinese Medicine, Dong-Qing-Nan Road, Guiyang, 550025, Guizhou Province, China
| | - Lucas Zellmer
- Department of Medicine, Hennepin County Medical Center, 730 South 8th St., Minneapolis, MN, 55415, USA
| | - Guangxue Meng
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Na Chen
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Hong Ma
- Department of Oral and Maxillofacial Surgery, School of Stomatology, Guizhou Medical University, 9 Beijing Road, Guiyang, 550004, Guizhou Province, China
| | - Zhe Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Air Force Medical University, 169 Changle West Road, Xi'an, 710032, China
| | - Dezhong Joshua Liao
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, 4 Beijing Rd, Guiyang, 550004, Guizhou Province, China
- Key Lab of Endemic and Ethnic Diseases of the Ministry of Education of China in Guizhou Medical University, Guiyang, 550004, Guizhou Province, China
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3
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Quintero J, Saad NY, Pagnoni SM, Jacquelin DK, Gatica L, Harper SQ, Rosa AL. The DUX4 protein is a co-repressor of the progesterone and glucocorticoid nuclear receptors. FEBS Lett 2022; 596:2644-2658. [PMID: 35662006 DOI: 10.1002/1873-3468.14416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 11/09/2022]
Abstract
DUX4 is a transcription factor required during early embryonic development in placental mammals. In this work we provide evidence that DUX4 is a co-repressor of nuclear receptors (NRs) of progesterone (PR) and glucocorticoids (GR). The DUX4 C-ter and N-ter regions, including the nuclear localization signals and homeodomain motifs, contribute to the corepressor activity of DUX4 on PR and GR. Immunoprecipitation studies, using total protein extracts of cells expressing tagged versions of DUX4 and GR, support that these proteins are physically associated. Our studies suggest that DUX4 could modulate gene expression by coregulating the activity of hormone NRs. This is the first report highlighting a potential endocrine role for DUX4.
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Affiliation(s)
- Julieta Quintero
- Laboratorio de Genética y Biología Molecular, IRNASUS-CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina
| | - Nizar Y Saad
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Sabrina M Pagnoni
- Laboratorio de Genética y Biología Molecular, IRNASUS-CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina
| | - Daniela K Jacquelin
- Laboratorio de Genética y Biología Molecular, IRNASUS-CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina.,INFIQC-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Laura Gatica
- Laboratorio de Genética y Biología Molecular, IRNASUS-CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina.,CIBICI-CONICET, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Argentina
| | - Scott Q Harper
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Alberto L Rosa
- Laboratorio de Genética y Biología Molecular, IRNASUS-CONICET, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina.,Fundación Allende-CONICET, Córdoba, Argentina
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4
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Saad NY, Al-Kharsan M, Garwick-Coppens SE, Chermahini GA, Harper MA, Palo A, Boudreau RL, Harper SQ. Human miRNA miR-675 inhibits DUX4 expression and may be exploited as a potential treatment for Facioscapulohumeral muscular dystrophy. Nat Commun 2021; 12:7128. [PMID: 34880230 PMCID: PMC8654987 DOI: 10.1038/s41467-021-27430-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 11/18/2021] [Indexed: 01/02/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is a potentially devastating myopathy caused by de-repression of the DUX4 gene in skeletal muscles. Effective therapies will likely involve DUX4 inhibition. RNA interference (RNAi) is one powerful approach to inhibit DUX4, and we previously described a RNAi gene therapy to achieve DUX4 silencing in FSHD cells and mice using engineered microRNAs. Here we report a strategy to direct RNAi against DUX4 using the natural microRNA miR-675, which is derived from the lncRNA H19. Human miR-675 inhibits DUX4 expression and associated outcomes in FSHD cell models. In addition, miR-675 delivery using gene therapy protects muscles from DUX4-associated death in mice. Finally, we show that three known miR-675-upregulating small molecules inhibit DUX4 and DUX4-activated FSHD biomarkers in FSHD patient-derived myotubes. To our knowledge, this is the first study demonstrating the use of small molecules to suppress a dominant disease gene using an RNAi mechanism.
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Affiliation(s)
- Nizar Y. Saad
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Mustafa Al-Kharsan
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA ,grid.266832.b0000 0001 2188 8502Department of Neurology, University of New Mexico Health Sciences Center, Albuquerque, NM USA
| | - Sara E. Garwick-Coppens
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Gholamhossein Amini Chermahini
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Madison A. Harper
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Andrew Palo
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA
| | - Ryan L. Boudreau
- grid.214572.70000 0004 1936 8294Department of Internal Medicine, Fraternal Order of Eagles Diabetes Research Center, Abboud Cardiovascular Research Center, Carver College of Medicine, University of Iowa, Iowa City, IA USA
| | - Scott Q. Harper
- grid.240344.50000 0004 0392 3476Center for Gene Therapy, the Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH USA ,grid.261331.40000 0001 2285 7943Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH USA
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5
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Ciszewski L, Lu-Nguyen N, Slater A, Brennan A, Williams HEL, Dickson G, Searle MS, Popplewell L. G-quadruplex ligands mediate downregulation of DUX4 expression. Nucleic Acids Res 2020; 48:4179-4194. [PMID: 32182342 PMCID: PMC7192601 DOI: 10.1093/nar/gkaa146] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 01/29/2020] [Accepted: 03/03/2020] [Indexed: 12/26/2022] Open
Abstract
Abnormal DUX4 expression in skeletal muscles plays a key role in facioscapulohumeral muscular dystrophy (FSHD) pathogenesis, although the molecular mechanisms regulating DUX4 expression are not fully defined. Using bioinformatic analysis of the genomic DUX4 locus, we have identified a number of putative G-quadruplexes (GQs) forming sequences. Their presence was confirmed in synthetic oligonucleotiode sequences derived from the enhancer, promoter and transcript of DUX4 through circular dichroism and nuclear magnetic resonance analysis. We further examined the binding affinity of a naturally occurring GQ stabilizing compound, berberine, to these non-canonical genetic structures using UV–Vis and fluorescence spectroscopy. Subsequent in vitro study in FSHD patient myoblasts indicated that berberine treatment reduced DUX4 expression and also expression of genes normally switched on by DUX4. Further investigation in a mouse model overexpressing exogenous DUX4 confirmed the therapeutic effects of berberine in downregulating DUX4 protein expression, inhibiting muscle fibrosis, and consequently rescuing muscle function. Our data demonstrate for the first time that GQs are present in the DUX4 locus and that the GQ interactive ligand reduces DUX4 expression suggesting potential role of GQs in FSHD pathogenesis. Our work provides the basis of a novel therapeutic strategy for the treatment of FSHD.
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Affiliation(s)
- Lukasz Ciszewski
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Ngoc Lu-Nguyen
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Alex Slater
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Andrew Brennan
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Huw E L Williams
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - George Dickson
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
| | - Mark S Searle
- Centre for Biomolecular Sciences, School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, UK
| | - Linda Popplewell
- Department of Biological Sciences, Royal Holloway-University of London, Egham, Surrey TW20 0EX, UK
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6
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Induction of a local muscular dystrophy using electroporation in vivo: an easy tool for screening therapeutics. Sci Rep 2020; 10:11301. [PMID: 32647247 PMCID: PMC7347864 DOI: 10.1038/s41598-020-68135-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 06/09/2020] [Indexed: 01/19/2023] Open
Abstract
Intramuscular injection and electroporation of naked plasmid DNA (IMEP) has emerged as a potential alternative to viral vector injection for transgene expression into skeletal muscles. In this study, IMEP was used to express the DUX4 gene into mouse tibialis anterior muscle. DUX4 is normally expressed in germ cells and early embryo, and silenced in adult muscle cells where its pathological reactivation leads to Facioscapulohumeral muscular dystrophy. DUX4 encodes a potent transcription factor causing a large deregulation cascade. Its high toxicity but sporadic expression constitutes major issues for testing emerging therapeutics. The IMEP method appeared as a convenient technique to locally express DUX4 in mouse muscles. Histological analyses revealed well delineated muscle lesions 1-week after DUX4 IMEP. We have therefore developed a convenient outcome measure by quantification of the damaged muscle area using color thresholding. This method was used to characterize lesion distribution and to assess plasmid recirculation and dose–response. DUX4 expression and activity were confirmed at the mRNA and protein levels and through a quantification of target gene expression. Finally, this study gives a proof of concept of IMEP model usefulness for the rapid screening of therapeutic strategies, as demonstrated using antisense oligonucleotides against DUX4 mRNA.
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7
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Mitsuhashi H, Homma S, Beermann ML, Ishimaru S, Takeda H, Yu BK, Liu K, Duraiswamy S, Boyce FM, Miller JB. Efficient system for upstream mRNA trans-splicing to generate covalent, head-to-tail, protein multimers. Sci Rep 2019; 9:2274. [PMID: 30783185 PMCID: PMC6381186 DOI: 10.1038/s41598-018-36684-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/20/2018] [Indexed: 01/11/2023] Open
Abstract
We present a plasmid-based system in which upstream trans-splicing efficiently generates mRNAs that encode head-to-tail protein multimers. In this system, trans-splicing occurs between one of two downstream splice donors in the sequence encoding a C-terminal V5 epitope tag and an upstream splice acceptor in the 5′ region of the pCS2(+) host plasmid. Using deletion and fusion constructs of the DUX4 protein as an example, we found that this system produced trans-spliced mRNAs in which coding regions from independent transcripts were fused in phase such that covalent head-to-tail protein multimers were translated. For a cDNA of ~450 bp, about half of the expressed proteins were multimeric, with the efficiency of trans-splicing and extent of multimer expression decreasing as cDNA length increased. This system generated covalent heterodimeric proteins upon co-transfections of plasmids encoding separate proteins and did not require a long complementary binding domain to position mRNAs for trans-splicing. This plasmid-based trans-splicing system is adaptable to multiple gene delivery systems, and it presents new opportunities for investigating molecular mechanisms of trans-splicing, generating covalent protein multimers with novel functions within cells, and producing mRNAs encoding large proteins from split precursors.
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Affiliation(s)
- Hiroaki Mitsuhashi
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan.
| | - Sachiko Homma
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Mary Lou Beermann
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Satoshi Ishimaru
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan
| | - Hayato Takeda
- Department of Applied, Biochemistry School of Engineering, Tokai University Kanagawa, Yokohama, 259-1207, Japan
| | - Bryant K Yu
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Kevin Liu
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Swetha Duraiswamy
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA
| | - Frederick M Boyce
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Jeffrey Boone Miller
- Department of Neurology, Boston University School of Medicine Boston, Massachusetts, 02118, USA.
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8
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Giesige CR, Wallace LM, Heller KN, Eidahl JO, Saad NY, Fowler AM, Pyne NK, Al-Kharsan M, Rashnonejad A, Chermahini GA, Domire JS, Mukweyi D, Garwick-Coppens SE, Guckes SM, McLaughlin KJ, Meyer K, Rodino-Klapac LR, Harper SQ. AAV-mediated follistatin gene therapy improves functional outcomes in the TIC-DUX4 mouse model of FSHD. JCI Insight 2018; 3:123538. [PMID: 30429376 DOI: 10.1172/jci.insight.123538] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/10/2018] [Indexed: 01/08/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant or digenic disorder linked to derepression of the toxic DUX4 gene in muscle. There is currently no pharmacological treatment. The emergence of DUX4 enabled development of cell and animal models that could be used for basic and translational research. Since DUX4 is toxic, animal model development has been challenging, but progress has been made, revealing that tight regulation of DUX4 expression is critical for creating viable animals that develop myopathy. Here, we report such a model - the tamoxifen-inducible FSHD mouse model called TIC-DUX4. Uninduced animals are viable, born in Mendelian ratios, and overtly indistinguishable from WT animals. Induced animals display significant DUX4-dependent myopathic phenotypes at the molecular, histological, and functional levels. To demonstrate the utility of TIC-DUX4 mice for therapeutic development, we tested a gene therapy approach aimed at improving muscle strength in DUX4-expressing muscles using adeno-associated virus serotype 1.Follistatin (AAV1.Follistatin), a natural myostatin antagonist. This strategy was not designed to modulate DUX4 but could offer a mechanism to improve muscle weakness caused by DUX4-induced damage. AAV1.Follistatin significantly increased TIC-DUX4 muscle mass and strength even in the presence of DUX4 expression, suggesting that myostatin inhibition may be a promising approach to treat FSHD-associated weakness. We conclude that TIC-DUX4 mice are a relevant model to study DUX4 toxicity and, importantly, are useful in therapeutic development studies for FSHD.
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Affiliation(s)
- Carlee R Giesige
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA.,Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Lindsay M Wallace
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Kristin N Heller
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Jocelyn O Eidahl
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nizar Y Saad
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Allison M Fowler
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Nettie K Pyne
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mustafa Al-Kharsan
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Afrooz Rashnonejad
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | - Jacqueline S Domire
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Diana Mukweyi
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Sara E Garwick-Coppens
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Susan M Guckes
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - K John McLaughlin
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kathrin Meyer
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Louise R Rodino-Klapac
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Scott Q Harper
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, Ohio, USA.,Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
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9
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Abstract
PURPOSE OF REVIEW To construct a framework to understand the different molecular interventions for muscular dystrophy. RECENT FINDINGS The recent approval of antisense oligonucleotides treatment for Duchenne muscular dystrophy and spinal muscular atrophy and current clinical trials using recombinant adeno-associated virus for the treatment of those diseases suggests that we are at a tipping point where we are able to treat and potentially cure muscular dystrophies. Understanding the basic molecular pathogenesis of muscular dystrophies and the molecular biology of the treatment allows for critical evaluation of the proposed therapies.
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Affiliation(s)
- Ava Y Lin
- Department of Neurology, University of Washington, Box 356465, 1959 NE Pacific Street, Seattle, WA, 98195-6465, USA
| | - Leo H Wang
- Department of Neurology, University of Washington, Box 356465, 1959 NE Pacific Street, Seattle, WA, 98195-6465, USA.
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10
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Ansseau E, Vanderplanck C, Wauters A, Harper SQ, Coppée F, Belayew A. Antisense Oligonucleotides Used to Target the DUX4 mRNA as Therapeutic Approaches in FaciosScapuloHumeral Muscular Dystrophy (FSHD). Genes (Basel) 2017; 8:genes8030093. [PMID: 28273791 PMCID: PMC5368697 DOI: 10.3390/genes8030093] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 02/16/2017] [Accepted: 02/22/2017] [Indexed: 02/02/2023] Open
Abstract
FacioScapuloHumeral muscular Dystrophy (FSHD) is one of the most prevalent hereditary myopathies and is generally characterized by progressive muscle atrophy affecting the face, scapular fixators; upper arms and distal lower legs. The FSHD locus maps to a macrosatellite D4Z4 repeat array on chromosome 4q35. Each D4Z4 unit contains a DUX4 gene; the most distal of which is flanked by a polyadenylation site on FSHD-permissive alleles, which allows for production of stable DUX4 mRNAs. In addition, an open chromatin structure is required for DUX4 gene transcription. FSHD thus results from a gain of function of the toxic DUX4 protein that normally is only expressed in germ line and stem cells. Therapeutic strategies are emerging that aim to decrease DUX4 expression or toxicity in FSHD muscle cells. We review here the heterogeneity of DUX4 mRNAs observed in muscle and stem cells; and the use of antisense oligonucleotides (AOs) targeting the DUX4 mRNA to interfere either with transcript cleavage/polyadenylation or intron splicing. We show in primary cultures that DUX4-targeted AOs suppress the atrophic FSHD myotube phenotype; but do not improve the disorganized FSHD myotube phenotype which could be caused by DUX4c over-expression. Thus; DUX4c might constitute another therapeutic target in FSHD.
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Affiliation(s)
- Eugénie Ansseau
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Avenue du Champ de Mars 6, 7000-Mons, Belgium.
| | - Céline Vanderplanck
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Avenue du Champ de Mars 6, 7000-Mons, Belgium.
| | - Armelle Wauters
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Avenue du Champ de Mars 6, 7000-Mons, Belgium.
| | - Scott Q Harper
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43205, USA.
- Center for Gene Therapy, The Research Institute at Nationwide Children's Hospital, Columbus, OH 43205, USA.
| | - Frédérique Coppée
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Avenue du Champ de Mars 6, 7000-Mons, Belgium.
| | - Alexandra Belayew
- Laboratory of Molecular Biology, Research Institute for Health Sciences and Technology, University of Mons, Avenue du Champ de Mars 6, 7000-Mons, Belgium.
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Abstract
PURPOSE OF REVIEW This article describes the clinical characteristics, diagnosis, molecular pathogenesis, and treatment of facioscapulohumeral muscular dystrophy (FSHD). RECENT FINDINGS FSHD comprises two genetically distinct types that converge on a common downstream pathway of the expression of the toxic protein DUX4. Approximately 95% of patients have FSHD type 1 (FSHD1), in which loss of DNA repetitive elements (D4Z4 repeats) in the subtelomeric region of chromosome 4q causes decreased methylation and epigenetic derepression of DUX4, a gene contained within each D4Z4 repeat. FSHD type 2 (FSHD2) occurs through a deletion-independent mechanism but, similar to FSHD1, leads to decreased methylation and epigenetic derepression in the same region of chromosome 4q. Whereas FSHD1 is dominantly inherited, FSHD2 shows digenic inheritance, and about 80% of patients will have a mutation in the SMCHD1 gene. DUX4 lacks a polyadenylation signal, so both FSHD1 and FSHD2 only occur in the presence of permissive 4q polymorphisms, which provide a stabilizing polyadenylation sequence. FSHD is an epigenetic disease, and penetrance and severity are related to both the number of residual D4Z4 units and D4Z4 methylation. SUMMARY Recent consensus guidelines outline standards for care for FSHD, and identification of potential therapeutic targets have shifted emphasis in the research community toward drug development and clinical trial planning.
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Gatica LV, Rosa AL. A complex interplay of genetic and epigenetic events leads to abnormal expression of the DUX4 gene in facioscapulohumeral muscular dystrophy. Neuromuscul Disord 2016; 26:844-852. [PMID: 27816329 DOI: 10.1016/j.nmd.2016.09.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 09/13/2016] [Accepted: 09/16/2016] [Indexed: 12/16/2022]
Abstract
Facioscapulohumeral muscular dystrophy (FSHD), a prevalent inherited human myopathy, develops following a complex interplay of genetic and epigenetic events. FSHD1, the more frequent genetic form, is associated with: (1) deletion of an integral number of 3.3 Kb (D4Z4) repeated elements at the chromosomal region 4q35, (2) a specific 4q35 subtelomeric haplotype denominated 4qA, and (3) decreased methylation of cytosines at the 4q35-linked D4Z4 units. FSHD2 is most often caused by mutations at the SMCHD1 (Structural Maintenance of Chromosomes Hinge Domain 1) gene, on chromosome 18p11.32. FSHD2 individuals also carry the 4qA haplotype and decreased methylation of D4Z4 cytosines. Each D4Z4 unit contains a copy of the retrotransposed gene DUX4 (double homeobox containing protein 4). DUX4 gene functionality was questioned in the past because of its pseudogene-like structure, its location on repetitive telomeric DNA sequences (i.e. junk DNA), and the elusive nature of both the DUX4 transcript and the encoded protein, DUX4. It is now known that DUX4 is a nuclear-located transcription factor, which is normally expressed in germinal tissues. Aberrant DUX4 expression triggers a deregulation cascade inhibiting muscle differentiation, sensitizing cells to oxidative stress, and inducing muscle atrophy. A unifying pathogenic model for FSHD emerged with the recognition that the FSHD-permissive 4qA haplotype corresponds to a polyadenylation signal that stabilizes the DUX4 mRNA, allowing the toxic protein DUX4 to be expressed. This working hypothesis for FSHD pathogenesis highlights the intrinsic epigenetic nature of the molecular mechanism underlying FSHD as well as the pathogenic pathway connecting FSHD1 and FSHD2. Pharmacological control of either DUX4 gene expression or the activity of the DUX4 protein constitutes current potential rational therapeutic approaches to treat FSHD.
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Affiliation(s)
| | - Alberto Luis Rosa
- Laboratorio de Biología Celular y Molecular, Fundación Allende, Argentina; Servicio de Genética Médica y Laboratorio Diagnóstico Biología Molecular, Sanatorio Allende, Córdoba, Argentina; Laboratorio de Genética y Biología Molecular, Facultad de Ciencias Químicas, Universidad Católica de Córdoba, Argentina.
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Bao B, Maruyama R, Yokota T. Targeting mRNA for the treatment of facioscapulohumeral muscular dystrophy. Intractable Rare Dis Res 2016; 5:168-76. [PMID: 27672539 PMCID: PMC4995414 DOI: 10.5582/irdr.2016.01056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited autosomal dominant disorder characterized clinically by progressive muscle degeneration. Currently, no curative treatment for this disorder exists. FSHD patients are managed through physiotherapy to improve function and quality of life. Over the last two decades, FSHD has been better understood as a disease genetically characterized by a pathogenic contraction of a subset of macrosatellite repeats on chromosome 4. Specifically, several studies support an FSHD pathogenesis model involving the aberrant expression of the double homeobox protein 4 (DUX4) gene. Hence, potential therapies revolving around inhibition of DUX4 have been explored. One of the potential treatment options is the use of effective antisense oligonucleotides (AOs) to knockdown expression of the myopathic DUX4 gene and its downstream molecules including paired-like homeodomain transcription factor 1 (PITX1). Success in the suppression of PITX1 expression has already been demonstrated systemically in vivo in recent studies. In this article, we will review the pathogenesis of FSHD and the latest research involving the use of antisense knockdown therapy.
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Affiliation(s)
- Bo Bao
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB, Canada
| | - Rika Maruyama
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB, Canada
| | - Toshifumi Yokota
- Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB, Canada
- Muscular Dystrophy Canada Research Chair, University of Alberta, Edmonton AB, Canada
- Address correspondence to: Dr. Toshifumi Yokota; Department of Medical Genetics, School of Human Development, Faculty of Medicine and Dentistry, University of Alberta, Edmonton AB, Canada T6G 2H7. E-mail:
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